[2024-01-24 15:19:04,429] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:19:04,431] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:19:04,431] [INFO] DQC Reference Directory: /var/lib/cwl/stg378f8ac7-c15b-415d-b42e-0d042d845b72/dqc_reference
[2024-01-24 15:19:05,673] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:19:05,674] [INFO] Task started: Prodigal
[2024-01-24 15:19:05,675] [INFO] Running command: gunzip -c /var/lib/cwl/stgea447f3f-8852-444d-bbbd-17bd62485c68/GCF_006516955.1_ASM651695v1_genomic.fna.gz | prodigal -d GCF_006516955.1_ASM651695v1_genomic.fna/cds.fna -a GCF_006516955.1_ASM651695v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:19:20,519] [INFO] Task succeeded: Prodigal
[2024-01-24 15:19:20,520] [INFO] Task started: HMMsearch
[2024-01-24 15:19:20,520] [INFO] Running command: hmmsearch --tblout GCF_006516955.1_ASM651695v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg378f8ac7-c15b-415d-b42e-0d042d845b72/dqc_reference/reference_markers.hmm GCF_006516955.1_ASM651695v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:19:20,897] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:19:20,898] [INFO] Found 6/6 markers.
[2024-01-24 15:19:20,944] [INFO] Query marker FASTA was written to GCF_006516955.1_ASM651695v1_genomic.fna/markers.fasta
[2024-01-24 15:19:20,944] [INFO] Task started: Blastn
[2024-01-24 15:19:20,944] [INFO] Running command: blastn -query GCF_006516955.1_ASM651695v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg378f8ac7-c15b-415d-b42e-0d042d845b72/dqc_reference/reference_markers.fasta -out GCF_006516955.1_ASM651695v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:21,857] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:21,861] [INFO] Selected 14 target genomes.
[2024-01-24 15:19:21,862] [INFO] Target genome list was writen to GCF_006516955.1_ASM651695v1_genomic.fna/target_genomes.txt
[2024-01-24 15:19:21,872] [INFO] Task started: fastANI
[2024-01-24 15:19:21,872] [INFO] Running command: fastANI --query /var/lib/cwl/stgea447f3f-8852-444d-bbbd-17bd62485c68/GCF_006516955.1_ASM651695v1_genomic.fna.gz --refList GCF_006516955.1_ASM651695v1_genomic.fna/target_genomes.txt --output GCF_006516955.1_ASM651695v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:19:36,406] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:36,406] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg378f8ac7-c15b-415d-b42e-0d042d845b72/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:19:36,406] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg378f8ac7-c15b-415d-b42e-0d042d845b72/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:19:36,418] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:19:36,418] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:19:36,418] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Martelella alba	strain=BGMRC 2036	GCA_006516955.1	2590451	2590451	type	True	100.0	1635	1638	95	conclusive
Martelella radicis	strain=DSM 28101	GCA_014196625.1	1397476	1397476	type	True	79.8314	666	1638	95	below_threshold
Martelella endophytica	strain=YC6887	GCA_000960975.1	1486262	1486262	type	True	79.6952	675	1638	95	below_threshold
Martelella lutilitoris	strain=GH2-6	GCA_005924265.1	2583532	2583532	type	True	79.6855	676	1638	95	below_threshold
Martelella mediterranea	strain=MACL11	GCA_002043005.1	293089	293089	type	True	79.6283	609	1638	95	below_threshold
Martelella mediterranea	strain=DSM 17316	GCA_000376125.1	293089	293089	type	True	79.5776	609	1638	95	below_threshold
Martelella limonii	strain=NBRC 109441	GCA_013344475.1	1647649	1647649	type	True	79.4235	563	1638	95	below_threshold
Neorhizobium vignae	strain=CCBAU 05176	GCA_000732195.1	690585	690585	type	True	77.9737	324	1638	95	below_threshold
Rhizobium petrolearium	strain=DSM 26482	GCA_017873175.1	515361	515361	type	True	77.8816	310	1638	95	below_threshold
Shinella daejeonensis	strain=JCM 16236	GCA_024281235.1	659017	659017	type	True	77.8651	281	1638	95	below_threshold
Shinella curvata	strain=C3	GCA_022899935.1	1817964	1817964	type	True	77.8268	324	1638	95	below_threshold
Rhizobium lusitanum	strain=P1-7	GCA_900094565.1	293958	293958	suspected-type	True	77.6089	354	1638	95	below_threshold
Shinella yambaruensis	strain=DSM 18801	GCA_022899355.1	415996	415996	type	True	77.6021	367	1638	95	below_threshold
Hoeflea alexandrii	strain=DSM 16655	GCA_024105735.1	288436	288436	type	True	77.2279	256	1638	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:19:36,419] [INFO] DFAST Taxonomy check result was written to GCF_006516955.1_ASM651695v1_genomic.fna/tc_result.tsv
[2024-01-24 15:19:36,420] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:19:36,420] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:19:36,420] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg378f8ac7-c15b-415d-b42e-0d042d845b72/dqc_reference/checkm_data
[2024-01-24 15:19:36,421] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:19:36,467] [INFO] Task started: CheckM
[2024-01-24 15:19:36,467] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006516955.1_ASM651695v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006516955.1_ASM651695v1_genomic.fna/checkm_input GCF_006516955.1_ASM651695v1_genomic.fna/checkm_result
[2024-01-24 15:20:24,247] [INFO] Task succeeded: CheckM
[2024-01-24 15:20:24,249] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:20:24,271] [INFO] ===== Completeness check finished =====
[2024-01-24 15:20:24,271] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:20:24,272] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006516955.1_ASM651695v1_genomic.fna/markers.fasta)
[2024-01-24 15:20:24,272] [INFO] Task started: Blastn
[2024-01-24 15:20:24,272] [INFO] Running command: blastn -query GCF_006516955.1_ASM651695v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg378f8ac7-c15b-415d-b42e-0d042d845b72/dqc_reference/reference_markers_gtdb.fasta -out GCF_006516955.1_ASM651695v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:20:26,032] [INFO] Task succeeded: Blastn
[2024-01-24 15:20:26,036] [INFO] Selected 13 target genomes.
[2024-01-24 15:20:26,037] [INFO] Target genome list was writen to GCF_006516955.1_ASM651695v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:20:26,053] [INFO] Task started: fastANI
[2024-01-24 15:20:26,053] [INFO] Running command: fastANI --query /var/lib/cwl/stgea447f3f-8852-444d-bbbd-17bd62485c68/GCF_006516955.1_ASM651695v1_genomic.fna.gz --refList GCF_006516955.1_ASM651695v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006516955.1_ASM651695v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:20:41,155] [INFO] Task succeeded: fastANI
[2024-01-24 15:20:41,166] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:20:41,167] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_006516955.1	s__Martelella alba	100.0	1635	1638	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Martelella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_013184775.1	s__Martelella sp013184775	89.4844	1359	1638	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Martelella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196625.1	s__Martelella radicis	79.8185	668	1638	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Martelella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000960975.1	s__Martelella endophytica	79.6814	676	1638	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Martelella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005924265.1	s__Martelella lutilitoris	79.6576	678	1638	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Martelella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001578105.1	s__Martelella sp001578105	79.6401	685	1638	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Martelella	95.0	97.55	95.11	0.93	0.87	3	-
GCF_002043005.1	s__Martelella mediterranea	79.6293	609	1638	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Martelella	95.0	97.32	95.96	0.90	0.83	4	-
GCA_003001975.1	s__Martelella mediterranea_A	79.5123	643	1638	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Martelella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013344475.1	s__Martelella limonii	79.4018	566	1638	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Martelella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013459645.1	s__Martelella sp013459645	79.0328	615	1638	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Martelella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000732195.1	s__Neorhizobium vignae	77.9693	325	1638	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004341625.1	s__Rhizobium sp004341625	77.8249	296	1638	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	97.83	97.83	0.87	0.87	2	-
GCA_002307905.1	s__Allorhizobium sp002307905	77.309	251	1638	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:20:41,168] [INFO] GTDB search result was written to GCF_006516955.1_ASM651695v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:20:41,169] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:20:41,172] [INFO] DFAST_QC result json was written to GCF_006516955.1_ASM651695v1_genomic.fna/dqc_result.json
[2024-01-24 15:20:41,173] [INFO] DFAST_QC completed!
[2024-01-24 15:20:41,173] [INFO] Total running time: 0h1m37s